Abstract
Ecological relationships between bacteria mediate the services
that gut microbiomes provide to their hosts. Knowing the overall
direction and strength of these relationships is essential to
learn how ecology scales up to affect microbiome assembly,
dynamics, and host health. However, whether bacterial
relationships are generalizable across hosts or personalized to
individual hosts is debated. Here, we apply a robust,
multinomial logistic-normal modeling framework to extensive time
series data (5534 samples from 56 baboon hosts over 13 years) to
infer thousands of correlations in bacterial abundance in
individual baboons and test the degree to which bacterial
abundance correlations are 'universal'. We also compare these
patterns to two human data sets. We find that, most bacterial
correlations are weak, negative, and universal across hosts,
such that shared correlation patterns dominate over
host-specific correlations by almost twofold. Further, taxon
pairs that had inconsistent correlation signs (either positive
or negative) in different hosts always had weak correlations
within hosts. From the host perspective, host pairs with the
most similar bacterial correlation patterns also had similar
microbiome taxonomic compositions and tended to be genetic
relatives. Compared to humans, universality in baboons was
similar to that in human infants, and stronger than one data set
from human adults. Bacterial families that showed universal
correlations in human infants were often universal in baboons.
Together, our work contributes new tools for analyzing the
universality of bacterial associations across hosts, with
implications for microbiome personalization, community assembly,
and stability, and for designing microbiome interventions to
improve host health.
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